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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Thu, 5 Sep 2013 10:25:46 -0600

Hi,

On Mon, Sep 2, 2013 at 8:55 PM, qiao xue <xueqiaoup.gmail.com> wrote:

*> Dear Amber Users:
*

*> I have some problems when performing PCA. The follows is the script:
*

*>
*

*> trajin md1.mdcrd
*

*> rms previous .CA,C,N time 2
*

*> matrix covar .CA name cvmat out cvmat.dat
*

*> analyze matrix cvmat name evecs out evecs.dat vecs 25
*

*> projection modes evecs .CA out project.dat beg 1 end 2
*

Be aware that in a normal batch ptraj/cpptraj run all analysis happens

after the initial pass through trajectories is complete, so your

'projection' command will actually be processed *before* the 'analyze

matrix' command. You probably want to do the 'projection' in a

separate run using 'evecs.dat' generated with the 'analyze matrix'

command (note that in cpptraj you actually can do this in one run via

COORDS data sets).

*> The first question is: How could I know the total variance? I know
*

*> the largest eigenvalue, but I do not know the total variance. So I
*

*> could not get the ratio. And I do not know whether PC1 and PC2 can
*

*> explain the motion of the system.
*

If you want to know how much each eigenvector contributes to the total

fluctuation, you should calculate and print out all the eigenmodes

from the diagonalization of your coordinate covariance matrix (i.e.

all 3*N modes, where N is the number of atoms selected by mask '.CA'),

not just the first 25. Then you can sum up all of the eigenvalues and

calculate the fraction each one contributes.

*> The second question is: When I get the projection data. I found
*

*> that the data has big difference with any tutorials and literatures.
*

*> In tutorials, when ploting the datas into scatter diagram (X axis:PC1;
*

*> Y axis: PC2), the range of x and y axises are -2 nm to 2 nm. However,
*

*> in my scatter diagram, the range of the datas varied from -300 to 300.
*

First, there is no reason that the range of your projections should

match those from calculations perfromed on different systems with

differing #s of frames etc. It's difficult to say whether the results

are reasonable without knowing the size of your system, the # of

frames you are using etc.

*> And I do not know the unit of measurement. How could I get the correct
*

The units of a projection are Angstroms.

*> The last question is: I have N atoms to calculate. But the
*

*> covariance matrix dimension is 3N * 3N, this can not be used as the x,
*

*> y axis. How could I get the N * N covariance matrix?
*

I'm not sure what you mean by "can not be used as the x, y axis". You

can reduce the dimensionality of covariance eigenvectors from 3N to N

with the 'reduce' keyword (see the AmberTolls 13 manual for more

details). You can also calculate an NxN correlation matrix (aka a

DCCM) with 'matrix correl'.

Hope this helps,

-Dan

Date: Thu, 5 Sep 2013 10:25:46 -0600

Hi,

On Mon, Sep 2, 2013 at 8:55 PM, qiao xue <xueqiaoup.gmail.com> wrote:

Be aware that in a normal batch ptraj/cpptraj run all analysis happens

after the initial pass through trajectories is complete, so your

'projection' command will actually be processed *before* the 'analyze

matrix' command. You probably want to do the 'projection' in a

separate run using 'evecs.dat' generated with the 'analyze matrix'

command (note that in cpptraj you actually can do this in one run via

COORDS data sets).

If you want to know how much each eigenvector contributes to the total

fluctuation, you should calculate and print out all the eigenmodes

from the diagonalization of your coordinate covariance matrix (i.e.

all 3*N modes, where N is the number of atoms selected by mask '.CA'),

not just the first 25. Then you can sum up all of the eigenvalues and

calculate the fraction each one contributes.

First, there is no reason that the range of your projections should

match those from calculations perfromed on different systems with

differing #s of frames etc. It's difficult to say whether the results

are reasonable without knowing the size of your system, the # of

frames you are using etc.

The units of a projection are Angstroms.

I'm not sure what you mean by "can not be used as the x, y axis". You

can reduce the dimensionality of covariance eigenvectors from 3N to N

with the 'reduce' keyword (see the AmberTolls 13 manual for more

details). You can also calculate an NxN correlation matrix (aka a

DCCM) with 'matrix correl'.

Hope this helps,

-Dan

-- ------------------------- Daniel R. Roe, PhD Department of Medicinal Chemistry University of Utah 30 South 2000 East, Room 201 Salt Lake City, UT 84112-5820 http://home.chpc.utah.edu/~cheatham/ (801) 587-9652 (801) 585-9119 (Fax) _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Sep 05 2013 - 09:30:03 PDT

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